endoreg-db 0.8.6.4__py3-none-any.whl

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  1. endoreg_db/__init__.py +0 -0
  2. endoreg_db/admin.py +92 -0
  3. endoreg_db/api/serializers/finding_descriptions.py +0 -0
  4. endoreg_db/api/views/finding_descriptions.py +0 -0
  5. endoreg_db/api_urls.py +4 -0
  6. endoreg_db/apps.py +18 -0
  7. endoreg_db/assets/dummy_model.ckpt +1 -0
  8. endoreg_db/codemods/readme.md +88 -0
  9. endoreg_db/codemods/rename_datetime_fields.py +92 -0
  10. endoreg_db/config/__init__.py +0 -0
  11. endoreg_db/config/env.py +101 -0
  12. endoreg_db/data/__init__.py +144 -0
  13. endoreg_db/data/ai_model/data.yaml +7 -0
  14. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  15. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  16. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  17. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  18. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  19. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  20. endoreg_db/data/ai_model_type/data.yaml +7 -0
  21. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  22. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  23. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  24. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  25. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  26. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  27. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  28. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  29. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  30. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  31. endoreg_db/data/case_template/rule_value/.init +0 -0
  32. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  33. endoreg_db/data/case_template/template/base.yaml +8 -0
  34. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  35. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  36. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  37. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  38. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  39. endoreg_db/data/center/data.yaml +91 -0
  40. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  41. endoreg_db/data/center_shift/ukw.yaml +9 -0
  42. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  43. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  44. endoreg_db/data/db_summary.csv +58 -0
  45. endoreg_db/data/db_summary.xlsx +0 -0
  46. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  47. endoreg_db/data/disease/hepatology.yaml +5 -0
  48. endoreg_db/data/disease/misc.yaml +5 -0
  49. endoreg_db/data/disease/renal.yaml +5 -0
  50. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  51. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  52. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  53. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  54. endoreg_db/data/distribution/date/patient.yaml +7 -0
  55. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  56. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  57. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  58. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  59. endoreg_db/data/endoscope/data.yaml +93 -0
  60. endoreg_db/data/endoscope_type/data.yaml +11 -0
  61. endoreg_db/data/endoscopy_processor/data.yaml +50 -0
  62. endoreg_db/data/event/cardiology.yaml +15 -0
  63. endoreg_db/data/event/neurology.yaml +14 -0
  64. endoreg_db/data/event/surgery.yaml +13 -0
  65. endoreg_db/data/event/thrombembolism.yaml +20 -0
  66. endoreg_db/data/examination/examinations/data.yaml +72 -0
  67. endoreg_db/data/examination/time/data.yaml +48 -0
  68. endoreg_db/data/examination/time-type/data.yaml +8 -0
  69. endoreg_db/data/examination/type/data.yaml +17 -0
  70. endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
  71. endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
  72. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  73. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  74. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  75. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  76. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  77. endoreg_db/data/finding/complication.yaml +16 -0
  78. endoreg_db/data/finding/data.yaml +105 -0
  79. endoreg_db/data/finding/examination_setting.yaml +16 -0
  80. endoreg_db/data/finding/medication_related.yaml +18 -0
  81. endoreg_db/data/finding/outcome.yaml +12 -0
  82. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  83. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  84. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  85. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  86. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  87. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  88. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  89. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  90. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  91. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  92. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  93. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  94. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  95. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  96. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  97. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  98. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  99. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  100. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  101. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  102. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
  103. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  104. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  105. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  106. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
  107. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
  108. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
  109. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  110. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
  111. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
  112. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  113. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  114. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  115. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  116. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  117. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  118. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  119. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  120. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  121. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  122. endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
  123. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
  124. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
  125. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
  126. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
  127. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
  128. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  129. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  130. endoreg_db/data/finding_type/data.yaml +43 -0
  131. endoreg_db/data/gender/data.yaml +42 -0
  132. endoreg_db/data/information_source/annotation.yaml +6 -0
  133. endoreg_db/data/information_source/data.yaml +30 -0
  134. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  135. endoreg_db/data/information_source/medication.yaml +6 -0
  136. endoreg_db/data/information_source/prediction.yaml +7 -0
  137. endoreg_db/data/information_source_type/data.yaml +8 -0
  138. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  139. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  140. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  141. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  142. endoreg_db/data/lab_value/hematology.yaml +184 -0
  143. endoreg_db/data/lab_value/hormones.yaml +59 -0
  144. endoreg_db/data/lab_value/lipids.yaml +53 -0
  145. endoreg_db/data/lab_value/misc.yaml +76 -0
  146. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  147. endoreg_db/data/log_type/data.yaml +57 -0
  148. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  149. endoreg_db/data/lx_client_type/base.yaml +30 -0
  150. endoreg_db/data/lx_permission/base.yaml +24 -0
  151. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  152. endoreg_db/data/material/material.yaml +91 -0
  153. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  154. endoreg_db/data/medication/tah.yaml +70 -0
  155. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  156. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  157. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  158. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  159. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  160. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  161. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  162. endoreg_db/data/names_first/first_names.yaml +54 -0
  163. endoreg_db/data/names_last/last_names.yaml +51 -0
  164. endoreg_db/data/network_device/data.yaml +59 -0
  165. endoreg_db/data/network_device_type/data.yaml +12 -0
  166. endoreg_db/data/organ/data.yaml +29 -0
  167. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  168. endoreg_db/data/pdf_type/data.yaml +46 -0
  169. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  170. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  171. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  172. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  173. endoreg_db/data/profession/data.yaml +70 -0
  174. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  175. endoreg_db/data/qualification/m2.yaml +39 -0
  176. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  177. endoreg_db/data/qualification/sonography.yaml +36 -0
  178. endoreg_db/data/qualification_type/base.yaml +29 -0
  179. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  180. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  181. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  182. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
  183. endoreg_db/data/requirement/age.yaml +26 -0
  184. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  185. endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
  186. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
  187. endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
  188. endoreg_db/data/requirement/disease_misc.yaml +12 -0
  189. endoreg_db/data/requirement/disease_renal.yaml +96 -0
  190. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
  191. endoreg_db/data/requirement/event_cardiology.yaml +251 -0
  192. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  193. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  194. endoreg_db/data/requirement/gender.yaml +25 -0
  195. endoreg_db/data/requirement/lab_value.yaml +441 -0
  196. endoreg_db/data/requirement/medication.yaml +93 -0
  197. endoreg_db/data/requirement_operator/age.yaml +13 -0
  198. endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
  199. endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
  200. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  201. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  202. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
  203. endoreg_db/data/requirement_set_type/data.yaml +20 -0
  204. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  205. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  206. endoreg_db/data/risk/bleeding.yaml +26 -0
  207. endoreg_db/data/risk/thrombosis.yaml +37 -0
  208. endoreg_db/data/risk_type/data.yaml +27 -0
  209. endoreg_db/data/setup_config.yaml +38 -0
  210. endoreg_db/data/shift/endoscopy.yaml +21 -0
  211. endoreg_db/data/shift/m2.yaml +0 -0
  212. endoreg_db/data/shift_type/base.yaml +35 -0
  213. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  214. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  215. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  216. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  217. endoreg_db/data/unit/concentration.yaml +115 -0
  218. endoreg_db/data/unit/data.yaml +17 -0
  219. endoreg_db/data/unit/length.yaml +31 -0
  220. endoreg_db/data/unit/misc.yaml +20 -0
  221. endoreg_db/data/unit/rate.yaml +6 -0
  222. endoreg_db/data/unit/time.yaml +48 -0
  223. endoreg_db/data/unit/volume.yaml +35 -0
  224. endoreg_db/data/unit/weight.yaml +38 -0
  225. endoreg_db/data/waste/data.yaml +12 -0
  226. endoreg_db/exceptions.py +19 -0
  227. endoreg_db/factories/__init__.py +0 -0
  228. endoreg_db/forms/__init__.py +5 -0
  229. endoreg_db/forms/examination_form.py +11 -0
  230. endoreg_db/forms/patient_finding_intervention_form.py +18 -0
  231. endoreg_db/forms/patient_form.py +27 -0
  232. endoreg_db/forms/questionnaires/__init__.py +1 -0
  233. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  234. endoreg_db/forms/settings/__init__.py +8 -0
  235. endoreg_db/forms/unit.py +6 -0
  236. endoreg_db/helpers/__init__.py +0 -0
  237. endoreg_db/helpers/count_db.py +45 -0
  238. endoreg_db/helpers/data_loader.py +208 -0
  239. endoreg_db/helpers/default_objects.py +378 -0
  240. endoreg_db/helpers/download_segmentation_model.py +31 -0
  241. endoreg_db/helpers/interact.py +6 -0
  242. endoreg_db/helpers/test_video_helper.py +119 -0
  243. endoreg_db/logger_conf.py +140 -0
  244. endoreg_db/management/__init__.py +1 -0
  245. endoreg_db/management/commands/__init__.py +1 -0
  246. endoreg_db/management/commands/anonymize_video.py +0 -0
  247. endoreg_db/management/commands/check_auth.py +125 -0
  248. endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
  249. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  250. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  251. endoreg_db/management/commands/fix_video_paths.py +165 -0
  252. endoreg_db/management/commands/import_fallback_video.py +203 -0
  253. endoreg_db/management/commands/import_report.py +298 -0
  254. endoreg_db/management/commands/import_video.py +423 -0
  255. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  256. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  257. endoreg_db/management/commands/load_ai_model_data.py +77 -0
  258. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  259. endoreg_db/management/commands/load_base_db_data.py +192 -0
  260. endoreg_db/management/commands/load_center_data.py +68 -0
  261. endoreg_db/management/commands/load_contraindication_data.py +41 -0
  262. endoreg_db/management/commands/load_disease_classification_choices_data.py +41 -0
  263. endoreg_db/management/commands/load_disease_classification_data.py +41 -0
  264. endoreg_db/management/commands/load_disease_data.py +62 -0
  265. endoreg_db/management/commands/load_distribution_data.py +66 -0
  266. endoreg_db/management/commands/load_endoscope_data.py +68 -0
  267. endoreg_db/management/commands/load_event_data.py +41 -0
  268. endoreg_db/management/commands/load_examination_data.py +75 -0
  269. endoreg_db/management/commands/load_examination_indication_data.py +86 -0
  270. endoreg_db/management/commands/load_finding_data.py +128 -0
  271. endoreg_db/management/commands/load_gender_data.py +44 -0
  272. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +132 -0
  273. endoreg_db/management/commands/load_information_source.py +51 -0
  274. endoreg_db/management/commands/load_lab_value_data.py +50 -0
  275. endoreg_db/management/commands/load_medication_data.py +103 -0
  276. endoreg_db/management/commands/load_name_data.py +37 -0
  277. endoreg_db/management/commands/load_organ_data.py +43 -0
  278. endoreg_db/management/commands/load_pdf_type_data.py +61 -0
  279. endoreg_db/management/commands/load_profession_data.py +44 -0
  280. endoreg_db/management/commands/load_qualification_data.py +59 -0
  281. endoreg_db/management/commands/load_report_reader_flag_data.py +46 -0
  282. endoreg_db/management/commands/load_requirement_data.py +180 -0
  283. endoreg_db/management/commands/load_risk_data.py +56 -0
  284. endoreg_db/management/commands/load_shift_data.py +60 -0
  285. endoreg_db/management/commands/load_tag_data.py +57 -0
  286. endoreg_db/management/commands/load_unit_data.py +46 -0
  287. endoreg_db/management/commands/load_user_groups.py +28 -0
  288. endoreg_db/management/commands/register_ai_model.py +64 -0
  289. endoreg_db/management/commands/reset_celery_schedule.py +9 -0
  290. endoreg_db/management/commands/setup_endoreg_db.py +381 -0
  291. endoreg_db/management/commands/start_filewatcher.py +106 -0
  292. endoreg_db/management/commands/storage_management.py +548 -0
  293. endoreg_db/management/commands/summarize_db_content.py +189 -0
  294. endoreg_db/management/commands/validate_video.py +204 -0
  295. endoreg_db/management/commands/validate_video_files.py +161 -0
  296. endoreg_db/management/commands/video_validation.py +22 -0
  297. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  298. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  299. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
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  607. endoreg_db/tasks/video_ingest.py +157 -0
  608. endoreg_db/tasks/video_processing_tasks.py +327 -0
  609. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  610. endoreg_db/templates/admin/start_examination.html +12 -0
  611. endoreg_db/templates/timeline.html +176 -0
  612. endoreg_db/urls/__init__.py +83 -0
  613. endoreg_db/urls/anonymization.py +32 -0
  614. endoreg_db/urls/auth.py +16 -0
  615. endoreg_db/urls/classification.py +39 -0
  616. endoreg_db/urls/examination.py +54 -0
  617. endoreg_db/urls/files.py +6 -0
  618. endoreg_db/urls/label_video_segment_validate.py +33 -0
  619. endoreg_db/urls/label_video_segments.py +46 -0
  620. endoreg_db/urls/media.py +227 -0
  621. endoreg_db/urls/patient.py +19 -0
  622. endoreg_db/urls/report.py +48 -0
  623. endoreg_db/urls/requirements.py +13 -0
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  627. endoreg_db/urls/video.py +61 -0
  628. endoreg_db/urls.py +9 -0
  629. endoreg_db/utils/__init__.py +88 -0
  630. endoreg_db/utils/ai/__init__.py +9 -0
  631. endoreg_db/utils/ai/get.py +5 -0
  632. endoreg_db/utils/ai/inference_dataset.py +52 -0
  633. endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
  634. endoreg_db/utils/ai/postprocess.py +63 -0
  635. endoreg_db/utils/ai/predict.py +291 -0
  636. endoreg_db/utils/ai/preprocess.py +68 -0
  637. endoreg_db/utils/calc_duration_seconds.py +24 -0
  638. endoreg_db/utils/case_generator/__init__.py +0 -0
  639. endoreg_db/utils/case_generator/case_generator.py +159 -0
  640. endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
  641. endoreg_db/utils/case_generator/utils.py +30 -0
  642. endoreg_db/utils/check_video_files.py +148 -0
  643. endoreg_db/utils/cropping.py +29 -0
  644. endoreg_db/utils/dataloader.py +175 -0
  645. endoreg_db/utils/dates.py +60 -0
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  647. endoreg_db/utils/extract_specific_frames.py +72 -0
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  650. endoreg_db/utils/frame_anonymization_utils.py +463 -0
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  652. endoreg_db/utils/links/__init__.py +0 -0
  653. endoreg_db/utils/links/requirement_link.py +193 -0
  654. endoreg_db/utils/mime_types.py +0 -0
  655. endoreg_db/utils/names.py +76 -0
  656. endoreg_db/utils/ocr.py +190 -0
  657. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  658. endoreg_db/utils/paths.py +95 -0
  659. endoreg_db/utils/permissions.py +143 -0
  660. endoreg_db/utils/pipelines/Readme.md +235 -0
  661. endoreg_db/utils/pipelines/__init__.py +0 -0
  662. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  663. endoreg_db/utils/product/__init__.py +0 -0
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  666. endoreg_db/utils/pydantic_models/__init__.py +6 -0
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  669. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
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  675. endoreg_db/utils/validate_endo_roi.py +19 -0
  676. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  677. endoreg_db/utils/validate_video_detailed.py +357 -0
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  680. endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
  681. endoreg_db/utils/video/names.py +42 -0
  682. endoreg_db/utils/video/streaming_processor.py +312 -0
  683. endoreg_db/utils/video/video_splitter.py +94 -0
  684. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  685. endoreg_db/views/__init__.py +274 -0
  686. endoreg_db/views/anonymization/__init__.py +27 -0
  687. endoreg_db/views/anonymization/media_management.py +454 -0
  688. endoreg_db/views/anonymization/overview.py +216 -0
  689. endoreg_db/views/anonymization/validate.py +107 -0
  690. endoreg_db/views/auth/__init__.py +13 -0
  691. endoreg_db/views/auth/keycloak.py +113 -0
  692. endoreg_db/views/examination/__init__.py +33 -0
  693. endoreg_db/views/examination/examination.py +37 -0
  694. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  695. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  696. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  697. endoreg_db/views/examination/get_findings.py +41 -0
  698. endoreg_db/views/examination/get_instruments.py +18 -0
  699. endoreg_db/views/examination/get_interventions.py +14 -0
  700. endoreg_db/views/finding/__init__.py +9 -0
  701. endoreg_db/views/finding/finding.py +112 -0
  702. endoreg_db/views/finding/get_classifications.py +14 -0
  703. endoreg_db/views/finding/get_interventions.py +17 -0
  704. endoreg_db/views/finding_classification/__init__.py +13 -0
  705. endoreg_db/views/finding_classification/base.py +0 -0
  706. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  707. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  708. endoreg_db/views/label/__init__.py +5 -0
  709. endoreg_db/views/label/label.py +15 -0
  710. endoreg_db/views/label_video_segment/__init__.py +16 -0
  711. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  712. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  713. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  714. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  715. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  716. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  717. endoreg_db/views/label_video_segment/validate.py +226 -0
  718. endoreg_db/views/media/__init__.py +45 -0
  719. endoreg_db/views/media/pdf_media.py +388 -0
  720. endoreg_db/views/media/segments.py +71 -0
  721. endoreg_db/views/media/sensitive_metadata.py +314 -0
  722. endoreg_db/views/media/video_media.py +272 -0
  723. endoreg_db/views/media/video_segments.py +524 -0
  724. endoreg_db/views/meta/__init__.py +15 -0
  725. endoreg_db/views/meta/available_files_list.py +146 -0
  726. endoreg_db/views/meta/report_meta.py +53 -0
  727. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  728. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  729. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  730. endoreg_db/views/misc/__init__.py +63 -0
  731. endoreg_db/views/misc/center.py +13 -0
  732. endoreg_db/views/misc/csrf.py +7 -0
  733. endoreg_db/views/misc/gender.py +14 -0
  734. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  735. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  736. endoreg_db/views/misc/secure_url_validate.py +79 -0
  737. endoreg_db/views/misc/stats.py +220 -0
  738. endoreg_db/views/misc/translation.py +182 -0
  739. endoreg_db/views/misc/upload_views.py +240 -0
  740. endoreg_db/views/patient/__init__.py +5 -0
  741. endoreg_db/views/patient/patient.py +210 -0
  742. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  743. endoreg_db/views/patient_examination/__init__.py +11 -0
  744. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  745. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  746. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  747. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  748. endoreg_db/views/patient_examination/video.py +194 -0
  749. endoreg_db/views/patient_finding/__init__.py +7 -0
  750. endoreg_db/views/patient_finding/base.py +0 -0
  751. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  752. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  753. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  754. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  755. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  756. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  757. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  758. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  759. endoreg_db/views/pdf/__init__.py +8 -0
  760. endoreg_db/views/pdf/pdf_stream.py +186 -0
  761. endoreg_db/views/pdf/reimport.py +177 -0
  762. endoreg_db/views/report/__init__.py +9 -0
  763. endoreg_db/views/report/report_list.py +112 -0
  764. endoreg_db/views/report/report_with_secure_url.py +28 -0
  765. endoreg_db/views/report/start_examination.py +7 -0
  766. endoreg_db/views/requirement/__init__.py +10 -0
  767. endoreg_db/views/requirement/evaluate.py +279 -0
  768. endoreg_db/views/requirement/lookup.py +367 -0
  769. endoreg_db/views/requirement/lookup_store.py +252 -0
  770. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  771. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  772. endoreg_db/views/stats/__init__.py +13 -0
  773. endoreg_db/views/stats/stats_views.py +229 -0
  774. endoreg_db/views/video/__init__.py +59 -0
  775. endoreg_db/views/video/correction.py +530 -0
  776. endoreg_db/views/video/reimport.py +195 -0
  777. endoreg_db/views/video/segmentation.py +274 -0
  778. endoreg_db/views/video/task_status.py +49 -0
  779. endoreg_db/views/video/timeline.py +46 -0
  780. endoreg_db/views/video/video_analyze.py +52 -0
  781. endoreg_db/views/video/video_apply_mask.py +48 -0
  782. endoreg_db/views/video/video_correction.py +21 -0
  783. endoreg_db/views/video/video_download_processed.py +58 -0
  784. endoreg_db/views/video/video_examination_viewset.py +242 -0
  785. endoreg_db/views/video/video_meta.py +29 -0
  786. endoreg_db/views/video/video_processing_history.py +24 -0
  787. endoreg_db/views/video/video_remove_frames.py +48 -0
  788. endoreg_db/views/video/video_stream.py +306 -0
  789. endoreg_db/views.py +0 -0
  790. endoreg_db-0.8.6.4.dist-info/METADATA +383 -0
  791. endoreg_db-0.8.6.4.dist-info/RECORD +793 -0
  792. endoreg_db-0.8.6.4.dist-info/WHEEL +4 -0
  793. endoreg_db-0.8.6.4.dist-info/licenses/LICENSE +674 -0
endoreg_db/data/finding_classification/colonoscopy_location.yaml ADDED
@@ -0,0 +1,80 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "colonoscopy_location_default"
4
+ name_de: "Koloskopie Standard"
5
+ name_en: "Colonoscopy Default"
6
+ classification_types: [
7
+ "location",
8
+ ]
9
+ examinations: [
10
+ "colonoscopy"
11
+ ]
12
+ finding_types: [
13
+ "macroscopic"
14
+ ]
15
+ findings: [
16
+ "colon_polyp",
17
+ "tumor",
18
+ "erosion",
19
+ "ulcer",
20
+ "scar"
21
+ ]
22
+ choices: [
23
+ "terminal_ileum",
24
+ "cecum",
25
+ "ascending_colon",
26
+ "right_flexure",
27
+ "transverse_colon",
28
+ "descending_colon",
29
+ "sigmoid_colon",
30
+ "rectum",
31
+ "anal_canal"
32
+ ]
33
+
34
+ - model: endoreg_db.finding_classification
35
+ fields:
36
+ name: "colonoscopy_location_coarse"
37
+ name_de: "Koloskopie Grob"
38
+ name_en: "Colonoscopy Coarse"
39
+ classification_types: [
40
+ "location",
41
+ ]
42
+ examinations: [
43
+ "colonoscopy"
44
+ ]
45
+ finding_types: [
46
+ "macroscopic"
47
+ ]
48
+ findings: [
49
+ "colon_polyp",
50
+ # "tumor",
51
+ # "erosion",
52
+ # "ulcer",
53
+ # "scar"
54
+ ]
55
+ choices: [
56
+ "left_colon",
57
+ "right_colon",
58
+ "rectum"
59
+ ]
60
+
61
+ - model: endoreg_db.finding_classification
62
+ fields:
63
+ name: "colonoscopy_austria_screening_location"
64
+ name_de: "Koloskopie Österreich Screening Lokalisation"
65
+ name_en: "Colonoscopy Austria Screening Location"
66
+ classification_types: [
67
+ "location",
68
+ ]
69
+ examinations: [
70
+ "colonoscopy_austria_screening"
71
+ ]
72
+ findings: [
73
+ "colon_polyp",
74
+ ]
75
+ choices: [
76
+ "left_colon",
77
+ "right_colon",
78
+ "sigmoid_colon",
79
+ "rectum",
80
+ ]
endoreg_db/data/finding_classification/colonoscopy_lst.yaml ADDED
@@ -0,0 +1,21 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "colon_lesion_lst"
4
+ classification_types: [
5
+ "colon_lesion_shape",
6
+ "morphology"
7
+ ]
8
+ name_de: "Oberflächenklassifikation Kolonläsion"
9
+ name_en: "Colon Lesion Surface Classification"
10
+ examinations: [
11
+ "colonoscopy"
12
+ ]
13
+ findings: [
14
+ "colon_polyp",
15
+ ]
16
+ choices: [
17
+ "colon_lesion_lst_granular_homogeneous",
18
+ "colon_lesion_lst_granular_nodular_mixed",
19
+ "colon_lesion_lst_non_granular_flat_elevated",
20
+ "colon_lesion_lst_non_granular_pseudodepressed"
21
+ ]
endoreg_db/data/finding_classification/colonoscopy_nice.yaml ADDED
@@ -0,0 +1,20 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "colon_lesion_nice"
4
+ classification_types: [
5
+ "colon_lesion_advanced_imaging",
6
+ "morphology"
7
+ ]
8
+ name_de: "Kolonläsion - NICE"
9
+ name_en: "Colon lesion - NICE"
10
+ examinations: [
11
+ "colonoscopy"
12
+ ]
13
+ findings: [
14
+ "colon_polyp",
15
+ ]
16
+ choices: [
17
+ "colon_lesion_NICE_type_1",
18
+ "colon_lesion_NICE_type_2",
19
+ "colon_lesion_NICE_type_3"
20
+ ]
endoreg_db/data/finding_classification/colonoscopy_paris.yaml ADDED
@@ -0,0 +1,26 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "colon_lesion_paris"
5
+ classification_types: [
6
+ "colon_lesion_shape",
7
+ "morphology"
8
+ ]
9
+ name_de: "Formklassifikation Kolonläsion"
10
+ name_en: "Colon Lesion Shape Classification"
11
+ examinations: [
12
+ "colonoscopy"
13
+ ]
14
+ findings: [
15
+ "colon_polyp",
16
+ ]
17
+ choices: [
18
+ "colon_paris_Is", # maps to colon_lesion_planarity_sessile
19
+ "colon_paris_Ip", # colon_lesion_planarity_pedunculated
20
+ "colon_paris_IIa",
21
+ "colon_paris_IIb",
22
+ "colon_paris_IIc",
23
+ "colon_paris_III",
24
+ "colon_paris_IIa_IIc",
25
+ "colon_paris_IIb_IIc"
26
+ ]
endoreg_db/data/finding_classification/colonoscopy_sano.yaml ADDED
@@ -0,0 +1,22 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "colon_lesion_kudo"
5
+ classification_types: [
6
+ "colon_lesion_capillary_pattern",
7
+ "morphology"
8
+ ]
9
+ name_de: "Oberflächenklassifikation Kolonläsion"
10
+ name_en: "Colon Lesion Surface Classification"
11
+ examinations: [
12
+ "colonoscopy"
13
+ ]
14
+ findings: [
15
+ "colon_polyp",
16
+ ]
17
+ choices: [
18
+ "colon_lesion_sano_1",
19
+ "colon_lesion_sano_2",
20
+ "colon_lesion_sano_3a",
21
+ "colon_lesion_sano_3b",
22
+ ]
endoreg_db/data/finding_classification/colonoscopy_summary.yaml ADDED
@@ -0,0 +1,53 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "colonoscopy_not_complete_reason"
5
+ classification_types: []
6
+ examinations: [
7
+ "colonoscopy",
8
+ "colonoscopy_austria_screening",
9
+ ]
10
+ findings: [
11
+ "colonoscopy_complete",
12
+ ]
13
+ choices: [
14
+ "colonoscopy_incomplete_insufficient_preparation",
15
+ "colonoscopy_incomplete_complication",
16
+ "colonoscopy_incomplete_pain",
17
+ "colonoscopy_incomplete_stenosis",
18
+ "colonoscopy_incomplete_other",
19
+ ]
20
+
21
+ - model: endoreg_db.finding_classification
22
+ fields:
23
+ name: "colonoscopy_austria_screening_findings_summary_worst"
24
+ classification_types: []
25
+ examinations: [
26
+ "colonoscopy_austria_screening",
27
+ ]
28
+ findings: [
29
+ "colonoscopy_austria_screening_findings_summary",
30
+ ]
31
+ choices: [
32
+ "colonoscopy_worst_finding_colon_cancer",
33
+ "colonoscopy_worst_finding_other",
34
+ "colonoscopy_worst_finding_polyp",
35
+ "colonoscopy_worst_finding_rectum_cancer",
36
+ ]
37
+
38
+ - model: endoreg_db.finding_classification
39
+ fields:
40
+ name: "colonoscopy_screening_outcome_overall"
41
+ classification_types: []
42
+ examinations: [
43
+ "colonoscopy_austria_screening",
44
+ ]
45
+ findings: [
46
+ "colonoscopy_austria_screening_outcome",
47
+ ]
48
+ choices: [
49
+ "outcome_restitutio_ad_integrum",
50
+ "outcome_death",
51
+ "outcome_unknown",
52
+ "outcome_lasting_disability",
53
+ ]
endoreg_db/data/finding_classification/complication_generic.yaml ADDED
@@ -0,0 +1,25 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "complication_generic_type"
5
+ classification_types: []
6
+ examinations: [
7
+ "gastroscopy",
8
+ "endosonography_upper_gi",
9
+ "endosonography_lower_gi",
10
+ "ercp",
11
+ "small_bowel_endoscopy",
12
+ "capsule_endoscopy",
13
+ "percutaneous_transhepatic_biliary_drainage",
14
+ "colonoscopy",
15
+ "colonoscopy_austria_screening",
16
+ ]
17
+ findings: [
18
+ "complication",
19
+ ]
20
+ choices: [
21
+ "complication_generic_type_cardiorespiratory",
22
+ "complication_generic_type_bleeding",
23
+ "complication_generic_type_perforation",
24
+ "complication_generic_type_other",
25
+ ]
endoreg_db/data/finding_classification/examination_setting_generic.yaml ADDED
@@ -0,0 +1,40 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "examination_setting_generic_location"
5
+ classification_types: []
6
+ examinations: [
7
+ "gastroscopy",
8
+ "endosonography_upper_gi",
9
+ "endosonography_lower_gi",
10
+ "ercp",
11
+ "small_bowel_endoscopy",
12
+ "capsule_endoscopy",
13
+ "percutaneous_transhepatic_biliary_drainage",
14
+ "colonoscopy",
15
+ ]
16
+ findings: [
17
+ "examination_setting",
18
+ ]
19
+ choices: [
20
+ "examination_setting_generic_location_inpatient",
21
+ "examination_setting_generic_location_outpatient",
22
+ ]
23
+
24
+
25
+ - model: endoreg_db.finding_classification
26
+ fields:
27
+ name: "colonoscopy_austria_screening_final_examination_setting"
28
+ classification_types: []
29
+ examinations: [
30
+ "colonoscopy_austria_screening",
31
+ ]
32
+ findings: [
33
+ "examination_setting",
34
+ ]
35
+ choices: [
36
+ "examination_setting_generic_location_inpatient",
37
+ "examination_setting_generic_location_outpatient",
38
+ "examination_setting_operative",
39
+ "examination_setting_conservative"
40
+ ]
endoreg_db/data/finding_classification/histology_colo.yaml ADDED
@@ -0,0 +1,51 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "colonoscopy_polyp_histology"
4
+ classification_types: []
5
+ examinations: [
6
+ "colonoscopy",
7
+ "colonoscopy_austria_screening",
8
+ ]
9
+ findings: [
10
+ "colon_polyp",
11
+ ]
12
+ choices: [
13
+ "histology_polyp_hyperplastic",
14
+ "histology_polyp_adenoma_tubular",
15
+ "histology_polyp_adenoma_tubulovillous",
16
+ "histology_polyp_adenoma_villous",
17
+ "histology_polyp_sessile_serrated_lesion"
18
+ ]
19
+
20
+ - model: endoreg_db.finding_classification_choice
21
+ fields:
22
+ name: "colonoscopy_polyp_histology_dysplasia"
23
+ classification_types: []
24
+ examinations: [
25
+ "colonoscopy",
26
+ "colonoscopy_austria_screening",
27
+ ]
28
+ findings: [
29
+ "colon_polyp",
30
+ ]
31
+ choices: [
32
+ "histology_dysplasia_none",
33
+ "histology_dysplasia_low_grade",
34
+ "histology_dysplasia_high_grade",
35
+ ]
36
+
37
+ - model: endoreg_db.finding_classification
38
+ fields:
39
+ name: "colonoscopy_histology_dignity"
40
+ classification_types: []
41
+ examinations: [
42
+ "colonoscopy",
43
+ "colonoscopy_austria_screening",
44
+ ]
45
+ findings: [
46
+ "colon_polyp",
47
+ ]
48
+ choices: [
49
+ "histology_dignity_benign",
50
+ "histology_dignity_malign",
51
+ ]
endoreg_db/data/finding_classification/intervention_required.yaml ADDED
@@ -0,0 +1,26 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "intervention_required"
5
+ classification_types: []
6
+ examinations: [
7
+ "gastroscopy",
8
+ "endosonography_upper_gi",
9
+ "endosonography_lower_gi",
10
+ "ercp",
11
+ "small_bowel_endoscopy",
12
+ "capsule_endoscopy",
13
+ "percutaneous_transhepatic_biliary_drainage",
14
+ "colonoscopy",
15
+ "colonoscopy_austria_screening",
16
+ ]
17
+ findings: [
18
+ "colon_polyp",
19
+ "post-intervention-wound",
20
+ "ulcer",
21
+
22
+ ]
23
+ choices: [
24
+ "yes",
25
+ "no",
26
+ ]
endoreg_db/data/finding_classification/medication_related.yaml ADDED
@@ -0,0 +1,23 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "sedation_performed"
5
+ classification_types: []
6
+ examinations: [
7
+ "gastroscopy",
8
+ "endosonography_upper_gi",
9
+ "endosonography_lower_gi",
10
+ "ercp",
11
+ "small_bowel_endoscopy",
12
+ "capsule_endoscopy",
13
+ "percutaneous_transhepatic_biliary_drainage",
14
+ "colonoscopy",
15
+ "colonoscopy_austria_screening",
16
+ ]
17
+ findings: [
18
+ "sedation",
19
+ ]
20
+ choices: [
21
+ "yes",
22
+ "no",
23
+ ]
endoreg_db/data/finding_classification/visualized.yaml ADDED
@@ -0,0 +1,33 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "visualized"
5
+ classification_types: []
6
+ examinations: [
7
+ "gastroscopy",
8
+ "endosonography_upper_gi",
9
+ "endosonography_lower_gi",
10
+ "ercp",
11
+ "small_bowel_endoscopy",
12
+ "capsule_endoscopy",
13
+ "percutaneous_transhepatic_biliary_drainage",
14
+ "colonoscopy",
15
+ "colonoscopy_austria_screening",
16
+ ]
17
+ findings: [
18
+ "cecum",
19
+ "terminal_ileum",
20
+ "ileocecal_valve",
21
+ "ascending_colon",
22
+ "right_flexure",
23
+ "transverse_colon",
24
+ "left_flexure",
25
+ "descending_colon",
26
+ "sigmoid_colon",
27
+ "rectum",
28
+ "rectum_anus",
29
+ ]
30
+ choices: [
31
+ "yes",
32
+ "no",
33
+ ]
endoreg_db/data/finding_classification_choice/bowel_preparation.yaml ADDED
@@ -0,0 +1,78 @@
1
+ # Boston
2
+ - model: endoreg_db.finding_classification_choice
3
+ fields:
4
+ name: "bowel_prep_boston_0"
5
+ name_de: "0"
6
+ name_en: "bowel_prep_boston_0"
7
+
8
+ - model: endoreg_db.finding_classification_choice
9
+ fields:
10
+ name: "bowel_prep_boston_1"
11
+ name_de: "1"
12
+ name_en: "bowel_prep_boston_1"
13
+
14
+ - model: endoreg_db.finding_classification_choice
15
+ fields:
16
+ name: "bowel_prep_boston_2"
17
+ name_de: "2"
18
+ name_en: "bowel_prep_boston_2"
19
+
20
+ - model: endoreg_db.finding_classification_choice
21
+ fields:
22
+ name: "bowel_prep_boston_3"
23
+ name_de: "3"
24
+ name_en: "bowel_prep_boston_3"
25
+
26
+ # Aronchick
27
+ - model: endoreg_db.finding_classification_choice
28
+ fields:
29
+ name: "bowel_prep_aronchick_0"
30
+ name_de: "Inadäquat"
31
+ name_en: "Inadequate"
32
+
33
+ - model: endoreg_db.finding_classification_choice
34
+ fields:
35
+ name: "bowel_prep_aronchick_1"
36
+ name_en: "Fair"
37
+ name_de: "Ausreichend"
38
+
39
+ - model: endoreg_db.finding_classification_choice
40
+ fields:
41
+ name: "bowel_prep_aronchick_2"
42
+ name_en: "Good"
43
+ name_de: "Gut"
44
+
45
+ - model: endoreg_db.finding_classification_choice
46
+ fields:
47
+ name: "bowel_prep_aronchick_3"
48
+ name_en: "Excellent"
49
+ name_de: "Exzellent"
50
+
51
+ # Screening Austria
52
+ # Choices are "bowel_prep_perfect", "bowel_prep_good",
53
+ # "bowel_prep_fair", "bowel_prep_poor", "bowel_prep_poor_in_rc_only"
54
+ - model: endoreg_db.finding_classification_choice
55
+ fields:
56
+ name: "bowel_prep_perfect"
57
+ name_de: "Perfekt"
58
+ name_en: "Perfect"
59
+ - model: endoreg_db.finding_classification_choice
60
+ fields:
61
+ name: "bowel_prep_good"
62
+ name_de: "Gut"
63
+ name_en: "Good"
64
+ - model: endoreg_db.finding_classification_choice
65
+ fields:
66
+ name: "bowel_prep_fair"
67
+ name_de: "Befriedigend"
68
+ name_en: "Fair"
69
+ - model: endoreg_db.finding_classification_choice
70
+ fields:
71
+ name: "bowel_prep_poor"
72
+ name_de: "Schlecht"
73
+ name_en: "Poor"
74
+ - model: endoreg_db.finding_classification_choice
75
+ fields:
76
+ name: "bowel_prep_poor_in_rc_only"
77
+ name_de: "Schlecht (nur rechtes Kolon)"
78
+ name_en: "Poor (Right Colon Only)"
endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml ADDED
@@ -0,0 +1,32 @@
1
+ - model: endoreg_db.finding_morphology_classification_choice
2
+ fields:
3
+ name: "colon_lesion_circularity_false"
4
+ name_de: "Kolonläsion - Zirkularität"
5
+ name_en: "Colon lesion - circularity"
6
+ description: "Category for non-circular lesions"
7
+
8
+ - model: endoreg_db.finding_morphology_classification_choice
9
+ fields:
10
+ name: "colon_lesion_circularity_true"
11
+ name_de: "Kolonläsion - Zirkularität"
12
+ name_en: "Colon lesion - circularity"
13
+ description: "Category for circular lesions"
14
+ numerical_descriptors:
15
+ length:
16
+ unit: "milimeter"
17
+ min: 0
18
+ max: 100
19
+ default: null
20
+ distribution: "uniform"
21
+ description: "Length of the lesion in mm"
22
+ required: true
23
+ circumference:
24
+ unit: "percent"
25
+ min: 33
26
+ max: 100
27
+ mean: 50
28
+ std: 10
29
+ default: null
30
+ distribution: "normal"
31
+ description: "Circumference of the lesion in %"
32
+ required: true
endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml ADDED
@@ -0,0 +1,15 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "colon_lesion_jnet_1"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "colon_lesion_jnet_2a"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "colon_lesion_jnet_2b"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "colon_lesion_jnet_3"
endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml ADDED
@@ -0,0 +1,23 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "colon_lesion_kudo_1"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "colon_lesion_kudo_2"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "colon_lesion_kudo_3s"
12
+ - model: endoreg_db.finding_classification_choice
13
+ fields:
14
+ name: "colon_lesion_kudo_3l"
15
+ - model: endoreg_db.finding_classification_choice
16
+ fields:
17
+ name: "colon_lesion_kudo_4"
18
+ - model: endoreg_db.finding_classification_choice
19
+ fields:
20
+ name: "colon_lesion_kudo_5i"
21
+ - model: endoreg_db.finding_classification_choice
22
+ fields:
23
+ name: "colon_lesion_kudo_5n"
endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml ADDED
@@ -0,0 +1,15 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "colon_lesion_lst_granular_homogeneous"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "colon_lesion_lst_granular_nodular_mixed"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "colon_lesion_lst_non_granular_flat_elevated"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "colon_lesion_lst_non_granular_pseudodepressed"
endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml ADDED
@@ -0,0 +1,17 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "colon_lesion_NICE_type_1"
4
+ name_de: "Kolonläsion - NICE Typ 1"
5
+ name_en: "Colon lesion - NICE type 1"
6
+
7
+ - model: endoreg_db.finding_classification_choice
8
+ fields:
9
+ name: "colon_lesion_NICE_type_2"
10
+ name_de: "Kolonläsion - NICE Typ 2"
11
+ name_en: "Colon lesion - NICE type 2"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "colon_lesion_NICE_type_3"
16
+ name_de: "Kolonläsion - NICE Typ 3"
17
+ name_en: "Colon lesion - NICE type 3"
endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml ADDED
@@ -0,0 +1,57 @@
1
+ - model: endoreg_db.finiding_morphology_classification_choice
2
+ fields:
3
+ name: "colon_paris_Is"
4
+ name_de: "Kolonläsion Formklassifikation (Paris Is)"
5
+ name_en: "Colon Lesion Shape Classification (Paris Is)"
6
+ description: "Shape classification for colon lesions (Paris Is)"
7
+
8
+ - model: endoreg_db.finiding_morphology_classification_choice
9
+ fields:
10
+ name: "colon_paris_Ip"
11
+ name_de: "Kolonläsion Formklassifikation (Paris Ip)"
12
+ name_en: "Colon Lesion Shape Classification (Paris Ip)"
13
+ description: "Shape classification for colon lesions (Paris Ip)"
14
+
15
+ - model: endoreg_db.finiding_morphology_classification_choice
16
+ fields:
17
+ name: "colon_paris_IIa"
18
+ name_de: "Kolonläsion Formklassifikation (Paris IIa)"
19
+ name_en: "Colon Lesion Shape Classification (Paris IIa)"
20
+ description: "Shape classification for colon lesions (Paris IIa)"
21
+
22
+ - model: endoreg_db.finiding_morphology_classification_choice
23
+ fields:
24
+ name: "colon_paris_IIb"
25
+ name_de: "Kolonläsion Formklassifikation (Paris IIb)"
26
+ name_en: "Colon Lesion Shape Classification (Paris IIb)"
27
+ description: "Shape classification for colon lesions (Paris IIb)"
28
+
29
+ - model: endoreg_db.finiding_morphology_classification_choice
30
+ fields:
31
+ name: "colon_paris_IIc"
32
+ name_de: "Kolonläsion Formklassifikation (Paris IIc)"
33
+ name_en: "Colon Lesion Shape Classification (Paris IIc)"
34
+ description: "Shape classification for colon lesions (Paris IIc)"
35
+
36
+ - model: endoreg_db.finiding_morphology_classification_choice
37
+ fields:
38
+ name: "colon_paris_III"
39
+ name_de: "Kolonläsion Formklassifikation (Paris III)"
40
+ name_en: "Colon Lesion Shape Classification (Paris III)"
41
+ description: "Shape classification for colon lesions (Paris III)"
42
+
43
+ # IIa+IIc
44
+ - model: endoreg_db.finiding_morphology_classification_choice
45
+ fields:
46
+ name: "colon_paris_IIa_IIc"
47
+ name_de: "Kolonläsion Formklassifikation (Paris IIa+IIc)"
48
+ name_en: "Colon Lesion Shape Classification (Paris IIa+IIc)"
49
+ description: "Shape classification for colon lesions (Paris IIa+IIc)"
50
+
51
+ # IIb+IIc
52
+ - model: endoreg_db.finiding_morphology_classification_choice
53
+ fields:
54
+ name: "colon_paris_IIb_IIc"
55
+ name_de: "Kolonläsion Formklassifikation (Paris IIb+IIc)"
56
+ name_en: "Colon Lesion Shape Classification (Paris IIb+IIc)"
57
+ description: "Shape classification for colon lesions (Paris IIb+IIc)"